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Biblioteca (s) : |
INIA Las Brujas. |
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Fecha : |
11/12/2018 |
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Actualizado : |
11/12/2018 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Autor : |
ZHANG, X.; LOURENCO, D.; AGUILAR, I.; LEGARRA, A.; MISZTAL, I. |
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Afiliación : |
XINYUE ZHANG, Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, United States; DANIELA LOURENCO, Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, United States; IGNACIO AGUILAR GARCIA, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ANDRÉS LEGARRA, INRA (Institut National de la Recherche Agronomique); IGNACY MISZTAL, Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, United States. |
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Título : |
Weighting strategies for single-step genomic BLUP: An iterative approach for accurate calculation of GEBV and GWAS. |
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Fecha de publicación : |
2016 |
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Fuente / Imprenta : |
Frontiers in Genetics, 19 August 2016, Volume 7, Issue AUG, Article number 151. OPEN ACCESS |
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ISSN : |
1664-8021 |
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DOI : |
10.3389/fgene.2016.00151 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received 15 May 2016 // Accepted 04 August 2016 // Published 19 August 2016.
Specialty section:
This article was submitted to Statistical Genetics and Methodology, a section of the journal Frontiers in Genetics. |
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Contenido : |
ABSTRACT.
Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. Default weights in WGBLUP or WssGBLUP are obtained iteratively based on single SNP effect squared (u2) and/or heterozygosity. When the weights are optimal, prediction accuracy, and ability to detect major SNP are maximized. The objective was to develop optimal weights for WGBLUP-based methods. We evaluated 5 new procedures that accounted for locus-specific or windows-specific variance to maximize accuracy of predicting genomic estimated breeding value (GEBV) and SNP effect. Simulated datasets consisted of phenotypes for 13,000 animals, including 1540 animals genotyped for 45,000 SNP. Scenarios with 5, 100, and 500 simulated quantitative trait loci (QTL) were considered. The 5 new procedures for SNP weighting were: (1) u2 plus a constant equal to the weight of the top SNP; (2) from a heavy-tailed distribution (similar to BayesA); (3) for every 20 SNP in a window along the whole genome, the largest effect (u2) among them; (4) the mean effect of every 20 SNP; and (5) the summation of every 20 SNP. Those methods were compared to the default WssGBLUP, GBLUP, BayesB, and BayesC. WssGBLUP methods were evaluated over 10 iterations. The accuracy of predicting GEBV was the correlation between true and estimated genomic breeding values for 300 genotyped animals from the last generation. The ability to detect the simulated QTL was also investigated. For most of the QTL scenarios, the accuracies obtained with all WssGBLUP procedures were higher compared to those from BayesB and BayesC, partly due to automatic inclusion of parent average in the former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.
© 2016 Zhang, Lourenco, Aguilar, Legarra and Misztal. MenosABSTRACT.
Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. Default weights in WGBLUP or WssGBLUP are obtained iteratively based on single SNP effect squared (u2) and/or heterozygosity. When the weights are optimal, prediction accuracy, and ability to detect major SNP are maximized. The objective was to develop optimal weights for WGBLUP-based methods. We evaluated 5 new procedures that accounted for locus-specific or windows-specific variance to maximize accuracy of predicting genomic estimated breeding value (GEBV) and SNP effect. Simulated datasets consisted of phenotypes for 13,000 animals, including 1540 animals genotyped for 45,000 SNP. Scenarios with 5, 100, and 500 simulated quantitative trait loci (QTL) were considered. The 5 new procedures for SNP weighting were: (1) u2 plus a constant equal to the weight of the top SNP; (2) from a heavy-tailed distribution (similar to BayesA); (3) for every 20 SNP in a window along the whole genome, the largest effect (u2) among them; (4) the mean effect of every 20 SNP; and (5) the summation of every 20 SNP. Those methods were compared to the default WssG... Presentar Todo |
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Palabras claves : |
BayesB; BayesC; GENOME-WIDE ASSOCIATION; SNP WINDOW; WssGBLUP. |
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Asunto categoría : |
-- |
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URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/12161/1/fgene-07-00151.pdf
https://www.frontiersin.org/articles/10.3389/fgene.2016.00151/full
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Marc : |
LEADER 03310naa a2200265 a 4500
001 1059369
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008 2016 bl uuuu u00u1 u #d
022 $a1664-8021
024 7 $a10.3389/fgene.2016.00151$2DOI
100 1 $aZHANG, X.
245 $aWeighting strategies for single-step genomic BLUP$bAn iterative approach for accurate calculation of GEBV and GWAS.$h[electronic resource]
260 $c2016
500 $aArticle history: Received 15 May 2016 // Accepted 04 August 2016 // Published 19 August 2016. Specialty section: This article was submitted to Statistical Genetics and Methodology, a section of the journal Frontiers in Genetics.
520 $aABSTRACT. Genomic Best Linear Unbiased Predictor (GBLUP) assumes equal variance for all single nucleotide polymorphisms (SNP). When traits are influenced by major SNP, Bayesian methods have the advantage of SNP selection. To overcome the limitation of GBLUP, unequal variance or weights for all SNP are applied in a method called weighted GBLUP (WGBLUP). If only a fraction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. Default weights in WGBLUP or WssGBLUP are obtained iteratively based on single SNP effect squared (u2) and/or heterozygosity. When the weights are optimal, prediction accuracy, and ability to detect major SNP are maximized. The objective was to develop optimal weights for WGBLUP-based methods. We evaluated 5 new procedures that accounted for locus-specific or windows-specific variance to maximize accuracy of predicting genomic estimated breeding value (GEBV) and SNP effect. Simulated datasets consisted of phenotypes for 13,000 animals, including 1540 animals genotyped for 45,000 SNP. Scenarios with 5, 100, and 500 simulated quantitative trait loci (QTL) were considered. The 5 new procedures for SNP weighting were: (1) u2 plus a constant equal to the weight of the top SNP; (2) from a heavy-tailed distribution (similar to BayesA); (3) for every 20 SNP in a window along the whole genome, the largest effect (u2) among them; (4) the mean effect of every 20 SNP; and (5) the summation of every 20 SNP. Those methods were compared to the default WssGBLUP, GBLUP, BayesB, and BayesC. WssGBLUP methods were evaluated over 10 iterations. The accuracy of predicting GEBV was the correlation between true and estimated genomic breeding values for 300 genotyped animals from the last generation. The ability to detect the simulated QTL was also investigated. For most of the QTL scenarios, the accuracies obtained with all WssGBLUP procedures were higher compared to those from BayesB and BayesC, partly due to automatic inclusion of parent average in the former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. © 2016 Zhang, Lourenco, Aguilar, Legarra and Misztal.
653 $aBayesB
653 $aBayesC
653 $aGENOME-WIDE ASSOCIATION
653 $aSNP WINDOW
653 $aWssGBLUP
700 1 $aLOURENCO, D.
700 1 $aAGUILAR, I.
700 1 $aLEGARRA, A.
700 1 $aMISZTAL, I.
773 $tFrontiers in Genetics, 19 August 2016, Volume 7, Issue AUG, Article number 151. OPEN ACCESS
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Registro original : |
INIA Las Brujas (LB) |
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Registro completo
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Biblioteca (s) : |
INIA Tacuarembó. |
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Fecha actual : |
12/10/2020 |
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Actualizado : |
13/10/2020 |
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Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
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Circulación / Nivel : |
Internacional - -- |
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Autor : |
POLI, C.H.E.C.; MONTEIRO, A.L.G.; DEVINCENZI, T.; ALBUQUERQUE, F.H.M.A.R.D.; MOTTA, J.H.D.; BORGES, L.I.; MUIR, J.P. |
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Afiliación : |
CESAR HENRIQUE ESPÍRITO CANDAL POLI, Departamento de Zootecnia, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; ALDA LUCIA GOMES MONTEIRO, Departamento de Zootecnia, Universidade Federal do Paraná, Curitiba, Brazil; THAIS DEVINCENZI, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; FERNANDO HENRIQUE MELO ANDRADE RODRIGUES DE ALBUQUERQUE, Embrapa Caprinos e Ovinos, Sobral, Brazil; JULIANO HENRIQUES DA MOTTA, Departamento de Zootecnia, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; LUIZA ILHA BORGES, Departamento de Zootecnia, Universidade Federal do Paraná, Curitiba, Brazil; JAMES PIERRE MUIR, Texas A&M AgriLife, Stephenville, TX, United States. |
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Título : |
Management Strategies for Lamb Production on Pasture-Based Systems in Subtropical Regions: A Review. |
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Fecha de publicación : |
2020 |
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Fuente / Imprenta : |
Frontiers in Veterinary Science, 15 September 2020, Volume 7, Article number 543. OPEN ACCESS. Doi: https://doi.org/10.3389/fvets.2020.00543 |
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DOI : |
10.3389/fvets.2020.00543 |
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Idioma : |
Inglés |
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Notas : |
Article history: Received: 30 March 2020; Accepted: 13 July 2020; Published: 15 September 2020. AUTHOR CONTRIBUTIONS: Every author had important contributions on this manuscript. The first CP and the second authors AM are the head of the research projects, being responsible for all parts of the
studies. The third author is a researcher TD, and the fourth, fifth, and sixth authors FA, JPM, and LB are Ph.D. students who developed the research review. The seventh author JPM is a professor who contributed to manuscript configuration and publication. All authors contributed to the article and approved
the submitted version. Correspondence: Cesar Henrique Espírito Candal Poli: cesar.poli@ufrgs.br |
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Contenido : |
Sheep production on pasture plays an important role in subtropical climates around the world, with great economic and environmental relevance to those regions. However, this production is much lower than its true potential in subtropical regions, largely due to lack of knowledge of how to feed grazing lambs, and mitigate gastrointestinal parasite infections. Due to weather instability and the high growth rate of tropical grasses, it is difficult to adjust the quality and quantity of feed consumed by lambs. In addition, due to warm, wet weather during spring, summer, and autumn, gastrointestinal parasite infection can be intense on subtropical pastures. Thus, the objective of this paper is to summarize 17 years of research in southern regions of Brazil testing alternative management for sheep farmers under these challenging conditions. Our review indicates that ewes play important roles raising their lambs. Besides protecting and providing milk, they leave a better pasture structure for lamb nutrition. The use of creep feeding and creep grazing are additional alternatives to improve lamb growth. However, feeding supplementation with concentrate can deteriorate pasture quality at the end of the summer?autumn season. Gastrointestinal parasitic infections can be reduced with improved lamb nutrition, although L3 larvae of Haemonchus contortus can be present at various pasture heights. This indicates that it is difficult to control L3 ingestion solely by manipulating grazing heights. We summarize important technologies for raising lambs on pasture-based systems to make the best of high herbage growth and minimize intense parasitic infections common in subtropical regions. We discuss research results in light of the latest studies from other ecoregions and climates, although there is a lack of similar research in subtropical regions of the world. MenosSheep production on pasture plays an important role in subtropical climates around the world, with great economic and environmental relevance to those regions. However, this production is much lower than its true potential in subtropical regions, largely due to lack of knowledge of how to feed grazing lambs, and mitigate gastrointestinal parasite infections. Due to weather instability and the high growth rate of tropical grasses, it is difficult to adjust the quality and quantity of feed consumed by lambs. In addition, due to warm, wet weather during spring, summer, and autumn, gastrointestinal parasite infection can be intense on subtropical pastures. Thus, the objective of this paper is to summarize 17 years of research in southern regions of Brazil testing alternative management for sheep farmers under these challenging conditions. Our review indicates that ewes play important roles raising their lambs. Besides protecting and providing milk, they leave a better pasture structure for lamb nutrition. The use of creep feeding and creep grazing are additional alternatives to improve lamb growth. However, feeding supplementation with concentrate can deteriorate pasture quality at the end of the summer?autumn season. Gastrointestinal parasitic infections can be reduced with improved lamb nutrition, although L3 larvae of Haemonchus contortus can be present at various pasture heights. This indicates that it is difficult to control L3 ingestion solely by manipulating grazing heigh... Presentar Todo |
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Palabras claves : |
CONCENTRATE SUPPLEMENT; EWE; OVINOS; PASTURAS; PASTURE MANAGEMENT; PERFORMANCE; SHEEP; SHEEP PRODUCTION. |
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Thesagro : |
OVEJAS. |
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Asunto categoría : |
L02 Alimentación animal |
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URL : |
https://www.frontiersin.org/articles/10.3389/fvets.2020.00543/pdf
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Marc : |
LEADER 03562naa a2200325 a 4500
001 1061410
005 2020-10-13
008 2020 bl uuuu u00u1 u #d
024 7 $a10.3389/fvets.2020.00543$2DOI
100 1 $aPOLI, C.H.E.C.
245 $aManagement Strategies for Lamb Production on Pasture-Based Systems in Subtropical Regions$bA Review.$h[electronic resource]
260 $c2020
500 $aArticle history: Received: 30 March 2020; Accepted: 13 July 2020; Published: 15 September 2020. AUTHOR CONTRIBUTIONS: Every author had important contributions on this manuscript. The first CP and the second authors AM are the head of the research projects, being responsible for all parts of the studies. The third author is a researcher TD, and the fourth, fifth, and sixth authors FA, JPM, and LB are Ph.D. students who developed the research review. The seventh author JPM is a professor who contributed to manuscript configuration and publication. All authors contributed to the article and approved the submitted version. Correspondence: Cesar Henrique Espírito Candal Poli: cesar.poli@ufrgs.br
520 $aSheep production on pasture plays an important role in subtropical climates around the world, with great economic and environmental relevance to those regions. However, this production is much lower than its true potential in subtropical regions, largely due to lack of knowledge of how to feed grazing lambs, and mitigate gastrointestinal parasite infections. Due to weather instability and the high growth rate of tropical grasses, it is difficult to adjust the quality and quantity of feed consumed by lambs. In addition, due to warm, wet weather during spring, summer, and autumn, gastrointestinal parasite infection can be intense on subtropical pastures. Thus, the objective of this paper is to summarize 17 years of research in southern regions of Brazil testing alternative management for sheep farmers under these challenging conditions. Our review indicates that ewes play important roles raising their lambs. Besides protecting and providing milk, they leave a better pasture structure for lamb nutrition. The use of creep feeding and creep grazing are additional alternatives to improve lamb growth. However, feeding supplementation with concentrate can deteriorate pasture quality at the end of the summer?autumn season. Gastrointestinal parasitic infections can be reduced with improved lamb nutrition, although L3 larvae of Haemonchus contortus can be present at various pasture heights. This indicates that it is difficult to control L3 ingestion solely by manipulating grazing heights. We summarize important technologies for raising lambs on pasture-based systems to make the best of high herbage growth and minimize intense parasitic infections common in subtropical regions. We discuss research results in light of the latest studies from other ecoregions and climates, although there is a lack of similar research in subtropical regions of the world.
650 $aOVEJAS
653 $aCONCENTRATE SUPPLEMENT
653 $aEWE
653 $aOVINOS
653 $aPASTURAS
653 $aPASTURE MANAGEMENT
653 $aPERFORMANCE
653 $aSHEEP
653 $aSHEEP PRODUCTION
700 1 $aMONTEIRO, A.L.G.
700 1 $aDEVINCENZI, T.
700 1 $aALBUQUERQUE, F.H.M.A.R.D.
700 1 $aMOTTA, J.H.D.
700 1 $aBORGES, L.I.
700 1 $aMUIR, J.P.
773 $tFrontiers in Veterinary Science, 15 September 2020, Volume 7, Article number 543. OPEN ACCESS. Doi: https://doi.org/10.3389/fvets.2020.00543
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INIA Tacuarembó (TBO) |
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